MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Rank	Gene	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 25 to 74 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Ranked	Divided	15	28	1.86667
		Squared	Subtracted	407289	263351	143938
	cytohesin 4. [swissprot;acc:q9uia0]	Measured		41482.5	33356.5	8126
	hbs1-like. [refseq;acc:nm_006620]		Divided	2597.5	698.5	3.71868
		Squared		1596.92	115.48	13.8285
		Rooted		50.9657	26.4292	1.92839
			Subtracted			24.5365
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Ranked		337	232	105
5	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Rooted		145.551	168.796	23.245
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Measured		41482.5	33356.5	8126
	cytohesin 4. [swissprot;acc:q9uia0]	Ranked	Divided	15	28	1.86667
		Squared	Subtracted	407289	263351	143938
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Measured	Divided	1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Ranked	Subtracted	212	309	97
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		Divided	15	28	1.86667
		Squared	Subtracted	407289	263351	143938
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Measured	Divided	1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]		Subtracted	145.551	168.796	23.245
	protein x 0004. [refseq;acc:nm_016301]	Ranked		212	309	97
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Measured		44490.5	36927.5	7563
7	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]			21185	28492	7307
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Ranked	Divided	215	322	1.49767
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared	Subtracted	310840	442993	132153
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Rooted		145.551	168.796	23.245
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Ranked		288.754	212.554	76.2
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	Measured	Divided	1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
8	db83 protein. [swissprot;acc:p57088]	Measured		1153.5	339.5	3.39764
		Squared		314.926	27.2805	11.544
		Rooted		33.9632	18.4255	1.84327
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Squared	Subtracted	250303	354894	104591
	hbs1-like. [refseq;acc:nm_006620]	Ranked	Divided	215	322	1.49767
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]		Subtracted	288	362	74
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Measured		21185	28492	7307
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Rooted		145.551	168.796	23.245
9	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Ranked		288	362	74
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted		145.551	168.796	23.245
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Measured		21185	28492	7307
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Squared		256169	162517	93652
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Measured	Divided	398.5	1281.5	3.21581
		Squared		37.5863	388.696	10.3414
		Rooted		19.9625	35.798	1.79326
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Ranked		212	309	1.45755
10	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Squared	Subtracted	219048	129762	89286
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Measured		21185	28492	7307

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.